Women under the age of 40 account for approximately 5% percent of breast cancer patients but numerous studies have shown that they have a worse prognosis and poorer outcome than women diagnosed at older ages. Breast tumors from young women are often ER-negative, from African-American patients and have other indicators of high risk: yet, multivariate analyses demonstrated that young age, in and of itself, is an independent predictor of poor outcome. At least partially due to the unique nature of the patient population served by DOD, a disproportionate number of breast cancer cases in young women are seen at WRNMMC. Thus CBCP has enrolled a good number of invasive breast cancer patients under 40 making it possible for us to propose this study. The CBCP Tissue Bank hosted at the Windber Research Institute has 40 tumors in OCT with germ line DNA available from blood clots for these sample. Thus there are sufficient numbers to get meaningful data. The tumors with germline DNA available will undergo whole exome sequencing and RNAseq. For tumors without matching germline DNA we will perform RNAseq only. We would also, as funding allows, to assess the samples using the OncoVar test developed by Dr. Meltzer which can test for mutation, deletions, and translocations in more than 250 genes known to be frequently mutated in solid tumors. The genomic analysis will be done in collaboration with Paul Meltzer at the NCI. These analyses will allow us to determine the spectrum of mutations seen in tumors from young women. All of these samples are clinically annotated into groups based on the clinical classification of the tumors (Luminal A, Luminal B, HER2+, and triple negative). For patients enrolled from the WRNMMC, most of the cases have outcome data and more outcome data is being collected. These analyses will be compared to the publically available databases for breast cancer (e.g. TCGA) in order to determine if the tumors have a different spectrum or frequency of mutations from those seen in older women or breast cancer as a whole. These data should help define the nature of the increased risk in young women as it could be due to differences in tumor genomics, or if there is no difference, it could be due to the environment in which the tumors arise. Thus the data will be informative in either case. Despite the poor prognosis of young women with breast cancer, little research and no clinical specific clinical trials are available. This project and its further development could represent a major advance in the field. Aim 2; Exploratory analysis of metaplastic and inflammatory breast cancer tumors. Metaplastic and inflammatory breast cancer are two rare (1% and 2-3%, respectively) types of aggressive breast cancer. For each of these, the mutations that drive these subtypes are not well characterized. Unfortunately, due to the low frequency of such tumors, there are only 4 of each of these in OCT (and only 3 of each with matching germline DNA) so that this Aim is an exploratory aim in which we will approach the tumors as above. For the 3 of each with matching DNA we will perform whole exome sequencing and RNAseq. For the samples without matching germline DNA, we will perform only RNAseq. Again, as funding permits we will use the OncoVar assay developed by Dr. Melzer. The existing samples are too few to give us a true spectrum of the diseases but could conceivable identify novel mutations that might be unique to these subsets. We will seek to expand these cohorts through collaboration with other institutions (e.g. JHU, WHC) to increase the sample size of each. Aim 3: Bioinformatic analysis of young women, metaplastic, and inflammatory breast cancer in the DOD databases. The DOD has clinical data in the linked MDR and DoD CCR databases on 14,588 breast cancer patients treated at DOD facilities between 1998-2007 (with future updates to include those treated through 2012). In collaboration with Dr. Kangmin Zhu at the MCC for Military Population Sciences and Epidemiology and assisted by Dr. Alexandra Zimmer from the WMB, we will use the database to investigate the incidence of the cancers in young women and track treatment and outcomes. If the numbers are sufficient, we will also explore these questions in metaplastic, and inflammatory cancers. The data from the DOD data bases has been presented as a poster discussion at the San Antonio Breast Cancer Symposium and a paper is in preparation.